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  Section: Genetics
 
 
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Genetics

 
     
 

Genetics : An Overview
Genetics : A study of heredity and variation
Sexuality : A source of hereditary variation
Ideas on heredity : A brief history
Ideas of Hippocrates and Aristotle
Preformation and epigenesist
Pangenes and acquired characters
Germplasm theory
Phenocopies
Scope and significance of genetics
Transmission genetics or classical genetics
Behavioural genetics
Developmental genetics
Forward genetics vs. reverse genetics


Mendel's Laws of Inheritance
Gregor Mendel's life
Pre-Mendelian experiments
Mendel's experiments
Symbols and terminology
Principle of segregation (law of purity of gametes)
Principle of independent assortment
Mendel's results, chromosome theory and linkage (present status)
Molecular basis of Mendel's wrinkled seed character
The rules of probability (product rule and sum rule)
Mendelian genetics in humans
Deviations from Mendel's finding


Lethality and Interaction of Genes
Lethality
Interaction of genes
Abbreviated genotypic ratio
Two gene pairs affecting same character
Epistasis
Complementary genes
Duplicate genes
Additional interactions involving two gene pairs
Interactions between more than two gene pairs
Modifiers, suppressors and pleiotropic genes
Meiotic drive, segregation distortion and selfish genes
Penetrance and expressivity


Quantitative Inheritance
Multiple factors
Binomial distribution
Effect of degree of dominance, number of genes and environment
Quantifying variability 
Variance and standard deviation
Partitioning of phenotypic variance
Heritability in broad sense and narrow sense


Multiple Alleles (Based on Classical Concept of Allelomorphism)
Multiple alleles and isoalleles 
Colour loci in corn
Skin colour in rodents
Eye colour in Drosophila
Self sterility in Nicotiana
ABO blood groups in humans


Physical Basis of Heredity 1.  The Nucleus and the Chromosome
The Nucleus 
Significance of nucleus : Hammerling's experiment
Number, shape and size of nucleus
Nucleus in prokaryotes and eukaryotes
Nuclear envelope
Nuclear pore complex and nucleocytoplasmic traffic
Nucleolus
Chromosomes
Number, size and shape of chromosomes
Morphology of chromosomes
Karyotypes
Euchromatin and heterochromatin
Constitutive and facultative heterochromatin
Single-stranded and multi-stranded hypotheses for chromosomes
Chemical composition of chromosomes
Infrastructure of chromosomes
Function of chromosomes
Special types of chromosomes 
Lampbrush chromosomes
Salivary gland chromosomes
B-Chromosomes
Prokaryotic Nucleoids


Physical Basis of Heredity 2.  Cell Division (Mitosis and Meiosis)
Mitosis
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis
Meiosis 
Significance of meiosis
Reproductive cycles
Stages of meiosis
Synaptonemal complex
Recombination nodules
Comparison of meiosis and mitosis


Physical Basis of Heredity 3.  Genetics, Biochemistry and Dynamics of Cell Division
Genetics of cell division cycle
Biochemistry of cell division 
Biochemistry of mitosis
Biochemistry of meiosis
Dynamics of chromosome movements during cell division
Events involving chromosome movement
Kinetochore and spindle in chromosome movement
Basic questions about kinetochore function


Physical Basis of Heredity 4. The Chromosome Theory of Inheritance
Association of paternal and maternal chromosomes at meiosis
Qualitative differences between chromosomes
Formulation of chromosome theory
Sex chromosomes and chromosome theory


Linkage and Crossing Over in Diploid Organisms (Higher Eukaryotes)
Coupling and repulsion hypothesis
A testcross in maize
Crossing over and meiosis 
Crossing over and chiasma formation
Mechanism of genetic recombination
Crossing over and linkage maps 
Recombination frequencies from a test-cross
Recombination frequencies from F2 data
Interference and coincidence
Linkage maps
Mapping function and poisson distribution
Linkage groups
Chi-square test 
Cytological basis of crossing over
Creighton and McClintock's experiment in corn
Meselson and Weigle's experiment using lambda (λ) phage
Crossing over at four strand stage


Tetrad Analysis, Mitotic Recombination and Gene Conversion in Haploid Organisms (Fungi and Single Celled Algae)
Tetrad analysis 
Analysis of ordered tetrads
Analysis of unordered tetrads
Mitotic recombination and parasexual cycle in Aspergillus 
Gene conversion.


Sexuality and Recombination in Bacteria and Viruses
Three Methods for Transfer of Genetic Material 
Sexual conjugation in bacteria 
Culture media and mutant strains
Discovery of gene transfer
Discovery of linkage in bacteria
Donor and recipient strains
- Mechanism of chromosome transfer
- Physical structures involved in chromosome transfer
Linkage maps in bacteria
Conjugation mapping through interrupted mapping
Circular linkage map
Linkage information from transformation
Recombination after gene transfer
High resolution mapping
Linear order of genes
Replication and recombination in viruses 
Replication of bacteriophages
Lysogenic bacteria
Transduction
Recombination in viruses
Circular genetic maps in viruses


Molecular Mechanisms of Recombination
Hybrid DNA models involving single strand breaks
Hybrid DNA models involving double strand breaks
Mismatch repair and post-meiotic segregation (pms) in heteroduplex region
Enzymes and proteins involved in recombination


Fine Structure of Gene-at the Genetic Level (A New Concept of Allelomorphism)
Gene vs allele : A new concept of allelomorphism 
Fine structure of gene (lozenge in Drosophila, rII in T4 phage)
Cistron, recon and muton


Plasmids, IS Elements, Transposons and Retroelements
Plasmids
Classification of plasmids
Replication, transfer and recombination in plasmids
Insertion sequences or IS elements
Transposons and controlling elements
Transposons in prokaryotes
Transposons in eukaryotes
Retrolelements (viral and non-viral)
Mechanism of Transposition
Uses of Transposons


Sex Linked, Sex Influenced and Sex Limited Traits
Sex linked traits 
Sex linkage in Drosophila
Sex linked lethals in Drosophila
Sex linkage in human beings
Sex linkage in poultry
Non-disjunction of sex chromosomes in Drosophila
Sex Influenced Traits (horned character in sheep)
Sex Limited Traits (cock feathering in poultry and baldness in man).


Sex Determination, Sex Differentiation, Dosage Compensation and Genetic Imprinting
Chromosome Theory of Sex Determination 
Balance Theory of Sex Determination X/A ratio in Drosophila
Triploid intersexes in Drosophila and genie balance theory
X/A ratio and gynandromorphs in Drosophila
X/A ratio in Coenorhabditis elegans (a free living nematode)
Balance Between Male and Female Factors
- Diploid intersexes in gypsy moth (Lymantria)
- X/A ratio and multiple numerator elements (Drosophila and Coenorhabditis)
Sex Determination in Plants
Methods for determining heterogametic sex in plants
Sex determination in Coccinia and Melandrium
Sex determination in other dioecious plants
Sex Chromosomes in Mammals Including Humans (Homo sapiens)
TDF, ZFY and SRY genes in humans
H-Y antigen and male development in mammals
Single gene control of sex
Sex determination in Asparagus
Tassel seed (ts) and silkless (sk) genes in maize
Transformer gene (tra)in Drosophila 
Haploid males in Hymenoptera
Hormonal control of sex
Environmental Sex Determination in Reptiles
Dosage Compensation in Organisms with Heterogametic Males
X-chromosome inactivation in mammals
Position effect variegation
Hyperactivity of X-chromosome in male Drosophila
Lack of Dosage Compensation in Organisms with Heterogametic Females
Genetic imprinting


Maternal Effects and Cytoplasmic Inheritance
Maternal effects
Cytoplasmic Inheritance Involving Dispensable Hereditary Units
Kappa particles in Paramecium
CO2 Sensitivity in Drosophila (sigma factor)
Organellar genetics 
Plastid inheritance : variegation in plants
Male sterility in plants
Chloroplast genetics Non-chromosomal genes in Chlamydomonas
Mitochondrial genetics
Paternal inheritance of cpDNA and mtDNA


Structural Changes in Chromosomes
Deficiencies
Duplications
Translocations 
Inversions 


Numerical Changes in Chromosomes
Aneuploidy 
Monosomy
Nullisomy
Trisomy
Tetrasomy
Euploidy 
Monoploidy and haploidy
Polyploidy


Mutations : 1.  Morphological Level (Including Lethal Mutations)
Brief History
Range of Mutations
Stages of Which Mutations Occur
Types of Mutations
Spontaneous Vs Induced Mutations
Mutation Rates and Frequencies
Induced Mutations 
Detection of Mutations in Drosophila 
Detection of Mutations in Plants
Use of Microbial Systems to Assess Potency of Mutagens
Practical Applications of Mutations
Effect of Genotypes on Induction of Mutations (Mutator Gene and Paramutations)
Adaptive Mutations and Genotrophs


Mutations : 2.  Biochemical Level (Biochemical and Microbial Genetics)
Inborn errors of metabolism in man
Eye transplantation in Drosophila
Biochemical mutations in Neurospora
Mutations in E. coli for resistance against phages or antibiotics
Cell counting in suspension
Calculation of mutation rates and frequencies
Biochemical mutations and biosynthetic pathways
Gene sequences and enzyme sequences in biosynthetic pathways


Mutations: 3.  Molecular Level (Mechanism)
Mutations and nucleotide sequences in nucleic acid 
Effect of chemical mutagens on nucleotide sequence
Effect of dyes on nucleotide sequence
Effect of physical conditions on nucleotide sequence
Effect of radiations on nucleotide sequence
Spontaneous mutations and nucleotide sequence
Mutation and amino acid sequences in proteins (including colinearity hypothesis)
Suppressor mutations, tRNAs and ribosomes


Human Genetics
Human chromosomes
Determination of sex
Sex linked inheritance
Chromosomal aberrations
Dizygotic and monozygotic twins
Inborn errors in metabolism
Sickle-cell anaemia
Genetic analysis through pedigree charts
Chromosome mapping in humans (including RFLPs, etc.)
Gene transfer in mammalian cells
Chromosome mediated gene transfer
Transformation of cells with free DNA
Use of human genetics in medical science 
Genetic counseling
Amniocentesis and antenatal diagnosis
Gene therapy
Making a choice of baby's sex
DNA fingerprinting in forensic science


Chemistry of the Gene 1.  Nucleic Acids and Their Structure
Nucleic acids as genetic material
Transformation experiments
Experiments with bacteriophage (T2) infection
Experiments with tobacco mosaic virus (TMV)
Structure of nucleic acids 
Bases
Nucleosides
Nucleotides
Polynucleotide
Deoxyribonucleic acid (DNA)
Alternative forms of DNA double helices
Z-DNA, a left handed DNA form
RL model
Supercoils in closed DNA
Ribonucleic acid (RNA)


Chemistry of the Gene 2.  Synthesis, Modification and Repair of DNA
DNA replication: general features 
Semi-conservative DNA replication in E. coli
Semi-conservative replication of chromosomes in eukaryotes
Semi-discontinuous DNA replication
Unidirectional and bidirectional DNA replication
RNA primers in DNA replication
Regulation of DNA replication by anti-sense RNA primer
Prokaryotic DNA polymerases
Eukaryotic DNA polymerases
Replicons for DNA replication
DNA replication in prokaryotes 
Experimental approaches for the study of DNA replication
Initiation of DNA replication
Elongation of DNA chain
Replication fork movement
Termination of DNA replication
DNA replication in eukaryotes 
DNA replication and cell cycle
Replication origins and initiation of DNA replication (cis and trans-acting elements)
Comparison of initiation of DNA replication with transcription initiation
Different steps involved in eukaryotic DNA replication
Synthesis of telomeric DNA by telomerase
Models of DNA replication
Replication fork model
Rolling circle model of DNA replication
Mitochondrial DNA replication and D-loops
RNA directed DNA synthesis (reverse transcription)
DNA modification and DNA restriction
DNA repair
Excision repair systems in E. coli
An SOS repair system in E. coli
DNA repair and genetic diseases in humans


Organization of Genetic Material 1.  Packaging of DNA as Nucleosomes in Eukaryotes
Techniques leading to nucleosome discovery
Subunit of chromatin - the nucleosome
Spatial arrangement of histones
Relation between different nucleosomes
Solenoid model
Loops, domains and scaffolds in chromatin
Chromatin replication and nucleosome assembly
Phasing and modification of nucleosomes in active genes


Organization of Genetic Material 2.  Repetitive and Unique DNA Sequences
Chromosomal DNA content and C-value paradox
Repetitive DNA 
Technique for detecting repetitive DNA
Chemical complexity vs sequence (kinetic) complexity
Repetitive DNA in the form of satellite DNA
Squash dot hybridization
Selfish DNA


Organization of Genetic Material 3.  Split Genes, Overlapping Genes and Pseudogenes
Split genes or interrupted genes 
Discovery and nature of split genes
R-loop mapping and restriction mapping of interrupted genes
Structure of chicken ovalbumin split gene
Split genes in fungal mitochondria
Split genes in chloroplasts
Intron of one gene may contain exon of another gene
Exon sequences are conserved, but intron sequences vary
Introns with coding sequences
Overlapping genes
Pseudogenes
Promiscuous DNA


The Genetic Code
Properties of genetic code 
Chain initiation and chain termination codons
Synonym codons and degeneracy
Mutations and the genetic code 
Wobble hypothesis
New genetic codes in mitochondria and ciliate protozoa
Suppressor mutations, base substitutions and suppressor tRNAs
Second genetic code, and second half of the genetic code
Recoding of the genetic code


Expression of Gene : Protein Synthesis 1.  Proteins and Protein Synthesis Apparatus (tRNA and Ribosomes)
Protein structure 
Primary structure of proteins
Secondary structure of proteins
Tertiary structure of proteins and 'second half of the genetic code'
Quaternary structure of proteins
Protein synthesis apparatus
Structure of tRNAs 
Structure of ribosomes 


Expression of Gene : Protein Synthesis 2.  Transcription in Prokaryotes and Eukaryotes
Transcription in prokaryotes 
Single RNA polymerase in E. coli
Promoter sites for initiation of transcription in prokaryotes
Initiation and elongation of RNA synthesis in prokaryotes
'Inchworm model' for elongation of transcript
Elongation arrest vs termination of transcription
Termination and antitermination of mRNA synthesis in prokaryotes
Transcription in eukaryotes 
Multiple RNA polymerases in eukaryotes
Promoter, enhancer and silencer sites for initiation of transcription in eukaryotes
Transcription factors and initiation of RNA synthesis in eukaryotes
Formation of preinitiation (transcription) complex with RNA polymerase II (Pol II)
Structure and role of TFIID and other transcription factors (TBP, TAFs)
TFIIB domains for interaction with TFIID/TATA complex
Phosphorylation of CTD of a subunit of Pol II
Formation of pre-initiation complex with Pol I and Pol III
Separate DNA binding and transcription activation domains
Transcription factors and elongation of RNA chains in eukaryotes
Chromatin structure and transcription
Transcription in mitochondria
Transcription of vertebrate mtDNA
Transcription of yeast and plant mtDNA
Transcription in chloroplasts


Expression of Gene : Protein Synthesis 3.  RNA Processing (RNA Splicing, RNA Editing and Ribozymes)
Addition of caps (m7G) and tails (polyA) for mRNA
Addition of methylated cap at the 5' end
Polyadenylation and the generation of 3' end
RNA splicing
Self-splicing of group I introns
Splicing of group II introns
Splicing of eukaryotic hnRNA through spliceosomes/snurposomes
Splicing of introns using RNA maturases or endonucleases
Yeast tRNA splicing by cutting and rejoining
Trans-splicing of transcripts in chloroplasts and mitochondria
Constitutive vs. alternative Splicing
RNA Editing and Guide RNA
Ribozymes 


Expression of Gene : Protein Synthesis 4. Translation in Prokaryotes and Eukaryotes
Formation of amino-acyl tRNA
Initiation of polypeptide 
Initiation in prokaryotes
Initiation in eukaryotes
Kozak's scanning hypothesis
Elongation of polypeptide
Binding of AA-tRNA at site 'A' of ribosome
Formation of peptide bond
Translocation of peptidyl tRNA from 'A' to 'P' site
Termination of polypeptide
Modification, folding and transport of released polypeptide
Translation in chloroplasts and mitochondria


Regulation of Gene Expression 1.  Operon Circuits in Bacteria and other Prokaryotes
Induction and repression
Inducer and co-repressor
The operon model for transcriptional regulation 
The tryptophan operon in bacteria (E. coli and Salmonella)
Tryptophan (trp) repressor controls three sets of genes
Negative and Positive Controls of Transcription
Substitution of Sigma Factor and Control of Transcription
Multiple sigma factors in E. coli 
Sporulation in bacteria
DNA sequences controlling transcription 
DNA sequences for CAP, RNA polymerase and lac-repressor
Identification of starting point
Pribnow box and other sequences common to DNA regions upstream to several operons
Regulation by DNA rearrangements
Post-transcriptional regulation
Leader sequences and attenuators
Autogenous regulation of translation
Regulation by alternative splicing
Regulation by-anti-sense RNA
Repression and activation of translation
Feedback inhibition
Signal transduction and ‘two component regulatory system’


Regulation of Gene Expression 2.  Cricuit of Lytic Cycle and Lysogeny in Bacteriophages
Regulation by a cascade in phages
Alternative sigma factors in phage SPO1
Lytic cascade in lambda (λ) phage
DNA binding of Cro and λ repressor proteins
Functional grouping of genes in phages T4 and T7


Regulation of Gene Expression 3. A Variety of Mechanisms in Eukaryotes
Regulation at Transcription Level
Activation of transcription
Britten-Davidson model for unit of transcription
Gene battery
Chromosomal proteins and gene expression
Repression of transcription 
Specific DNA sequences controlling transcription
Transgenic plants to study regulatory sequences
Modification of DNA sequences and their transcripts in gene expression
Alternative splicing of transcripts
Regulation at translation level
Activation and repression of translation
Masked mRNA in eggs of sea urchin and Xenopus
Regulation by gene re-arrangement
Expression of immunoglobulin genes
Yeast mating type switching
Trypanosome surface antigen (VSG) switching
Synthesis of mRNA in pieces in VSG genes in trypanosome
Regulation by reversible phosphorylation
Signal transduction and second messengers
Proteins and peptide hormonesand gene expression
Steroid hormones and gene expression
Interferon stimulated gene expression (without a second messenger)
Cell surface receptors in cholesterol metabolism and drug production
Ubiquitin protein and regulation of heat shock genes


Developmental Genetics
Factors controlling development
Changes in the Nucleus During Development (Nuclear Transplantation)
Turning genes on and off during development
Gene regulation during early embryonic development
The Genetics of Development
Developmental mutants in Drosophila
Developmental mutants in higher plants


Genetic Engineering and Biotechnology 1.  Recombinant DNA and PCR (Cloning and Amplification of DNA)
Restriction enzymes in cloning
Techniques used in recombinant DNA 
Cloning vectors for recombinant DNA
Plasmids as vectors
Bacteriophages as vectors
Plant and animal viruses as vectors
Transposons as vectors
Artificial chromosome vectors for cloning large DNA segments
Construction of chimeric DNA
Palindromes and staggered cleavage
Adding poly dA at the 3' ends of the vector and poly dT at the 3' ends of DNA clone
Blunt end ligation by T4 DNA ligase
Cloning in bacteria and eukaryotes
Cloning in bacteria
Cloning in eukaryotes
Molecular probes 
Labelling of probes
Applications of molecular probes
Construction and screening of genomic and cDNA libraries
Gene amplification : PCR and its applications
cDNA library from mRNA
Colony (or plaque) hybridization for screening of libraries
Gene Amplification : PCR and Its Applications
The basic polymerase chain reaction (PCR)
Different schemes of PCR


Genetic Engineering and Biotechnology 2.  Restriction Maps and Molecular Genetic Maps
Restriction mapping
Restriction cleavage and gel electrophoresis
Construction of a restriction map
Use of partial digests, end labeling and hybridization in restriction mapping
Restriction fragment length polymorphisms (RFLPs) as markers for genetic maps
Linkage and recombination between molecular and phenotypic markers
Random amplified polymorphic DNA (RAPDs) using PCR 
Minisatellites (VNTRs) and Microsatellites (SSRs)
Chromosome Walking and Characterization of Chromosome Segments
Reverse Genetics and Chromosome Jumping (or Hopping) Libraries


Genetic Engineering and Biotechnology 3.  Isolation, Sequencing and Synthesis of Genes
Isolation of genes 
Early attempts for isolation of ribosomal RNA genes in Xenopus
Isolation of genes coding for known specific proteins
Isolation of genes coding for an unknown product
Sequencing of genes or a DNA segment
Maxam and Gilbert's chemical degradation method
Synthesis of genes 
Chemical synthesis of genes
Synthesis of gene for yeast alanyl tRNA
Synthesis of gene for a true precursor tRNA
Gene synthesis machines


Genetic Engineering and Biotechnology 4.  Gene Transfer Methods and Transgenic Organisms
Gene transfer methods 
Gene transfer (transfection) methods in animals
Gene transfer methods in plants
Transgenic Organisms
Transgenic animals 
Transgenic plants 


Genetic Engineering and Biotechnology 5. Hybridoma and Monoclonal Antibodies
Hybridoma and the production of monoclonal antibodies
Improvements in hybridoma technology
Purification of antibodies
Antibody Engineering and Genetic Manipulations
Alternatives to hybridoma for monoclonal antibodies
Production of human and humanized antibodies
Uses of monoclonal antibodies
Monoclonal antibodies in diagnosis, screening and therapy
Vaccine production and monoclonal antibodies
Monoclonal antibodies as enzymes (abzymes)
Purification and quantitation of other molecules


Multigene Families in Eukaryotes
How is the demand for large quantities of gene product met?
Multigene families 
How to locate multigene families?
Multigene families with identical genes
Concerted evolution of multigene families 
Gene conversion
Sister chromatid exchange
Gene amplification


Genetics of Cancer : Proto-oncogenes, Oncogenes and Tumour Suppressor Genes
Viral oncogenes (y-onc genes)
Isolated oncogenes for transfection assay
Activation of proto-oncogenes by mutation
Activation of proto-oncogenes by insertions, translocations and amplification
Tumour suppressor genes or anti-oncogenes
Cellular functions of oncoproteins
Regulation of gene expression by oncoproteins
Signal transduction by oncoproteins (G proteins)


Population Genetics : Gene Frequencies in Populations
Gene pool and gene frequencies
Equilibrium of gene frequencies and Hardy-Weinberg 
Frequencies of two alleles at a single locus
Frequencies of more than two alleles at a single locus
Frequencies of alleles at two or more loci
Changes in gene frequencies 
Mutations
Selection
Balance between mutation and selection
Migration
Random drift


Inbreeding Depression and Heterosis
Inbreeding depression
Heterosis
Genetic basis of inbreeding depression and heterosis 
Application of heterosis


Genetic Basis of Evolution and Speciation
Theories of organic evolution 
Mutation theory
Synthetic theory
Evolution at molecular level
Evolution of proteins
Evolution of nucleotide sequences
Molecular evolution in test tube
Speciation 
Races
Species
Modes of speciation
 
     
 
 
     



     
 
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